Inside The New Flu VirusScientists tracking swine flu have discovered that the new virus emerged last fall and had been circulating undetected in Mexico until last month. Genetic analysis of the virus is proceeding at a furious pace. The aim is to find clues on what to expect if the virus re-emerges.

And ever since U.S. officials concerned with the health of humans discovered a new flu virus circulating in North America last month, scientists around the world have been testing its genes. That can reveal where the virus came from and, scientists hope, what kind of threat the virus represents.

NPR's Richard Knox reports that the project has already produced key findings.

RICHARD KNOX: The most important finding is that the newfound swine flu virus isn't as new as it first appeared. Oliver Pybus of Oxford University says the virus's genes reveal it's been circulating in Mexico for about eight months.

Dr. OLIVER PYBUS (Oxford University): The consistent range that we're getting out is the second half of last year, and the consistent best estimates are in the middle of that range, kind of around September, fall, last year.

KNOX: Pybus and his fellow scientists can tell by looking at how much the newly discovered virus has evolved from its ancestors. The likelihood that the virus was infecting people throughout Mexico's flu season is important.

Its presence was hidden by cases of regular flu and the absence of lab tests to identify the newcomer. That wouldn't have happened if the virus was causing lots of people to get very sick.

Genetic analysis also reveals that the virus is without doubt more related to swine flu viruses than anything else. Its great-granddaddy was a three-fer. Scientists call it a triple reassortant.

It was made up of genes from a classic swine virus that swapped genes from a seasonal human flu virus and a North American bird virus. That didn't happen anytime recently. Scientists say it was 10 or 20 years ago.

Joan Nichols says it's no accident that pigs played a big role. She's a swine flu expert at the University of Texas in Galveston.

Ms. JOAN NICHOLS (University of Texas, Galveston): Pigs are special because pigs can get infected with swine viruses, but they can also fairly easily be infected with avian strains or human strains, making pigs a mixing pot in a way.

KNOX: Pigs were also important in the novel virus's more recent evolution. Last year the triple virus combined with two other viruses that infect North American and Eurasian swine. Somehow that gave it the ability to infect humans. Pybus says this virus is a real genetic stew.

Mr. PYBUS: I learned a great word recently, gallimaufry, a hodgepodge of leftovers from a variety of sources. So perhaps we should call this the gallimaufry virus.

KNOX: So genetic analysis is giving the virus a back story, but scientists want to know if it can reveal the future too. Michael Worobey at the University of Arizona is paying special attention to the rate of changes in the virus's genetic code, and whether those alter the 10 proteins that make up the virus.

Mr. MICHAEL WOROBEY (University of Arizona): If we were seeing really rapid change, it might be more suggestive of a virus that was adapting to the human population in unpredictable ways that could lead to higher virulence, for instance. But so far we haven't seen any strong indication of that. I would say that that's reassuring.

KNOX: Virulence is the key question. It's the difference between a virus that can make a lot of people sick and kill some, and one that kills tens of millions like the pandemic flu virus of 1918.

Nobody knows more about virulence in flu viruses than Jeffery Taubenberger of the National Institutes of Health. He led an effort to reconstruct the 1918 virus out of genetic bits and pieces. Taubenberger says don't expect the genes of the swine flu virus to telegraph if it's evolving in a dangerous way.

Mr. JEFFERY TAUBENBERGER (National Institutes of Health): Virulence and the other behaviors of the virus are totally dependent on the overall genetic constellation and makeup of the virus.

KNOX: In other words, there's no mutation that's a red flag for virulence. Unfortunately, the only way to learn that will be to watch what the virus does to people in the Southern Hemisphere over the next few months. Their flu season is just beginning.

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